Nudt12 (nudix hydrolase 12) - Rat Genome Database

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Gene: Nudt12 (nudix hydrolase 12) Rattus norvegicus
Analyze
Symbol: Nudt12
Name: nudix hydrolase 12
RGD ID: 1310902
Description: Predicted to enable metal ion binding activity; phosphodiesterase decapping endonuclease activity; and pyrophosphatase activity. Predicted to be involved in RNA metabolic process; circadian regulation of gene expression; and nicotinamide nucleotide metabolic process. Predicted to be located in cytoplasm and nucleus. Predicted to be active in peroxisome. Orthologous to human NUDT12 (nudix hydrolase 12); PARTICIPATES IN niacin metabolic pathway; monoterpenoid biosynthetic pathway; INTERACTS WITH (+)-schisandrin B; 17beta-estradiol; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC367323; NAD-capped RNA hydrolase NUDT12; nudix (nucleoside diphosphate linked moiety X)-type motif 12; nudix-type motif 12; peroxisomal NADH pyrophosphatase NUDT12
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr89106,188,930 - 106,202,340 (-)NCBIGRCr8
mRatBN7.2998,741,627 - 98,755,039 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl998,742,360 - 98,755,039 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx9107,157,934 - 107,170,738 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.09112,285,705 - 112,298,509 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.09110,629,306 - 110,642,104 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.09105,680,603 - 105,693,374 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl9105,680,670 - 105,693,357 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.09105,282,066 - 105,294,901 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4997,551,943 - 97,565,919 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1997,763,808 - 97,773,230 (-)NCBI
Celera996,183,688 - 96,196,456 (-)NCBICelera
Cytogenetic Map9q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (ISO)
cytosol  (IEA)
nucleus  (IEA,ISO)
peroxisome  (IBA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
5. GOA pipeline RGD automated data pipeline
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12790796   PMID:31101919  


Genomics

Comparative Map Data
Nudt12
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr89106,188,930 - 106,202,340 (-)NCBIGRCr8
mRatBN7.2998,741,627 - 98,755,039 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl998,742,360 - 98,755,039 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx9107,157,934 - 107,170,738 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.09112,285,705 - 112,298,509 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.09110,629,306 - 110,642,104 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.09105,680,603 - 105,693,374 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl9105,680,670 - 105,693,357 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.09105,282,066 - 105,294,901 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4997,551,943 - 97,565,919 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1997,763,808 - 97,773,230 (-)NCBI
Celera996,183,688 - 96,196,456 (-)NCBICelera
Cytogenetic Map9q36NCBI
NUDT12
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385103,548,855 - 103,562,789 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5103,548,855 - 103,562,790 (-)EnsemblGRCh38hg38GRCh38
GRCh375102,884,556 - 102,898,490 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 365102,912,455 - 102,926,389 (-)NCBINCBI36Build 36hg18NCBI36
Build 345102,912,455 - 102,926,389NCBI
Celera598,832,394 - 98,846,327 (-)NCBICelera
Cytogenetic Map5q21.2NCBI
HuRef598,066,154 - 98,080,094 (-)NCBIHuRef
CHM1_15102,317,764 - 102,331,705 (-)NCBICHM1_1
T2T-CHM13v2.05104,057,169 - 104,071,102 (-)NCBIT2T-CHM13v2.0
Nudt12
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391759,307,104 - 59,320,317 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1759,306,613 - 59,320,367 (-)EnsemblGRCm39 Ensembl
GRCm381759,000,107 - 59,013,367 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1758,999,618 - 59,013,372 (-)EnsemblGRCm38mm10GRCm38
MGSCv371759,140,824 - 59,152,745 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361758,686,732 - 58,698,653 (-)NCBIMGSCv36mm8
Celera1763,340,740 - 63,352,661 (-)NCBICelera
Cytogenetic Map17DNCBI
cM Map1730.64NCBI
Nudt12
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541810,459,638 - 10,474,124 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541810,459,644 - 10,474,124 (+)NCBIChiLan1.0ChiLan1.0
NUDT12
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2498,832,811 - 98,846,787 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1596,986,459 - 97,000,835 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0598,903,740 - 98,917,763 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.15104,603,701 - 104,617,927 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5104,601,373 - 104,617,925 (-)Ensemblpanpan1.1panPan2
NUDT12
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.137,693,903 - 7,708,930 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl37,696,505 - 7,724,769 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha39,096,599 - 9,111,624 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.037,580,872 - 7,595,974 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl37,580,961 - 7,595,765 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.137,523,258 - 7,538,243 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.037,541,652 - 7,556,628 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.037,701,088 - 7,716,081 (+)NCBIUU_Cfam_GSD_1.0
Nudt12
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213162,779,449 - 162,793,749 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936523964,813 - 979,250 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936523964,858 - 979,118 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NUDT12
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl2109,045,592 - 109,059,616 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.12109,044,946 - 109,059,721 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22113,204,432 - 113,216,169 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NUDT12
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1236,980,848 - 6,995,193 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl236,978,704 - 6,994,660 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660367,322,532 - 7,336,519 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nudt12
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474321,701,158 - 21,717,123 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474321,702,453 - 21,716,805 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Nudt12
105 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1031
Count of miRNA genes:313
Interacting mature miRNAs:431
Transcripts:ENSRNOT00000066968
Prediction methods:Microtar, Miranda, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)925268044114175309Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)925661188100929786Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)956771635101771635Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)958163035100929646Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)961381434104821652Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)963869687108869687Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)964573531109573531Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)975712843111552878Rat
4889852Pur26Proteinuria QTL 26150.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)977813894101597663Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)977813894111552878Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)979271511102910209Rat
1582203Gluco19Glucose level QTL 193.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)992491589100929786Rat

Markers in Region
RH140172  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2998,742,400 - 98,742,590 (+)MAPPERmRatBN7.2
Rnor_6.09105,680,711 - 105,680,900NCBIRnor6.0
Rnor_5.09105,282,174 - 105,282,363UniSTSRnor5.0
RGSC_v3.4997,551,984 - 97,552,173UniSTSRGSC3.4
Celera996,183,729 - 96,183,918UniSTS
Cytogenetic Map9q36UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 6 23 16 2 16 12 27 9 1
Low 3 37 34 25 17 25 8 11 62 8 29 10 8
Below cutoff 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000066968   ⟹   ENSRNOP00000061974
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl998,742,360 - 98,755,039 (-)Ensembl
Rnor_6.0 Ensembl9105,680,670 - 105,693,357 (-)Ensembl
RefSeq Acc Id: NM_001109010   ⟹   NP_001102480
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr89106,189,661 - 106,202,340 (-)NCBI
mRatBN7.2998,742,360 - 98,755,039 (-)NCBI
Rnor_6.09105,680,670 - 105,693,357 (-)NCBI
Rnor_5.09105,282,066 - 105,294,901 (-)NCBI
RGSC_v3.4997,551,943 - 97,565,919 (-)RGD
Celera996,183,688 - 96,196,456 (-)RGD
Sequence:
RefSeq Acc Id: XM_006245588   ⟹   XP_006245650
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr89106,188,930 - 106,202,332 (-)NCBI
mRatBN7.2998,741,627 - 98,755,031 (-)NCBI
Rnor_6.09105,680,603 - 105,693,374 (-)NCBI
Rnor_5.09105,282,066 - 105,294,901 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039084014   ⟹   XP_038939942
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr89106,188,930 - 106,202,321 (-)NCBI
mRatBN7.2998,741,627 - 98,752,865 (-)NCBI
RefSeq Acc Id: XM_039084015   ⟹   XP_038939943
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr89106,188,930 - 106,202,332 (-)NCBI
mRatBN7.2998,741,627 - 98,755,031 (-)NCBI
RefSeq Acc Id: XM_063267546   ⟹   XP_063123616
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr89106,188,930 - 106,202,309 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001102480   ⟸   NM_001109010
- UniProtKB: D4A2H8 (UniProtKB/TrEMBL),   A6JR91 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006245650   ⟸   XM_006245588
- Peptide Label: isoform X1
- UniProtKB: D4A2H8 (UniProtKB/TrEMBL),   A6JR91 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000061974   ⟸   ENSRNOT00000066968
RefSeq Acc Id: XP_038939943   ⟸   XM_039084015
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038939942   ⟸   XM_039084014
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063123616   ⟸   XM_063267546
- Peptide Label: isoform X2
Protein Domains
Nudix hydrolase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A2H8-F1-model_v2 AlphaFold D4A2H8 1-462 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13696893
Promoter ID:EPDNEW_R7417
Type:multiple initiation site
Name:Nudt12_1
Description:nudix hydrolase 12
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.09105,693,331 - 105,693,391EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310902 AgrOrtholog
BioCyc Gene G2FUF-26574 BioCyc
Ensembl Genes ENSRNOG00000022576 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066968 ENTREZGENE
  ENSRNOT00000066968.3 UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.20 UniProtKB/TrEMBL
  3.90.79.20 UniProtKB/TrEMBL
  Nucleoside Triphosphate Pyrophosphohydrolase UniProtKB/TrEMBL
InterPro Ankyrin_rpt UniProtKB/TrEMBL
  Ankyrin_rpt-contain_sf UniProtKB/TrEMBL
  NADH_PPase-like_N UniProtKB/TrEMBL
  NudC-like_C UniProtKB/TrEMBL
  NUDIX_hydrolase_CS UniProtKB/TrEMBL
  NUDIX_hydrolase_dom UniProtKB/TrEMBL
  NUDIX_hydrolase_dom-like UniProtKB/TrEMBL
  Znr_NADH_PPase UniProtKB/TrEMBL
KEGG Report rno:367323 UniProtKB/TrEMBL
NCBI Gene 367323 ENTREZGENE
PANTHER NAD-CAPPED RNA HYDROLASE NUDT12 UniProtKB/TrEMBL
  NUDIX HYDROLASE, NUDC SUBFAMILY UniProtKB/TrEMBL
Pfam Ank_2 UniProtKB/TrEMBL
  NUDIX UniProtKB/TrEMBL
  NUDIX-like UniProtKB/TrEMBL
  zf-NADH-PPase UniProtKB/TrEMBL
PhenoGen Nudt12 PhenoGen
PROSITE ANK_REP_REGION UniProtKB/TrEMBL
  ANK_REPEAT UniProtKB/TrEMBL
  NUDIX UniProtKB/TrEMBL
  NUDIX_BOX UniProtKB/TrEMBL
RatGTEx ENSRNOG00000022576 RatGTEx
SMART ANK UniProtKB/TrEMBL
Superfamily-SCOP ANK UniProtKB/TrEMBL
  NUDIX_hydrolase UniProtKB/TrEMBL
UniProt A6JR91 ENTREZGENE, UniProtKB/TrEMBL
  D4A2H8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-10 Nudt12  nudix hydrolase 12  Nudt12  nudix (nucleoside diphosphate linked moiety X)-type motif 12  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Nudt12  nudix (nucleoside diphosphate linked moiety X)-type motif 12   Nudt12_predicted  nudix (nucleoside diphosphate linked moiety X)-type motif 12 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Nudt12_predicted  nudix (nucleoside diphosphate linked moiety X)-type motif 12 (predicted)      Symbol and Name status set to approved 70820 APPROVED